ASH (Alignment of Structural Homologs) is a structure alignment program that has been developed for PDBj. Earlier versions of ASH were written by Hiroyuki Toh[1]. The core alignment algorithm based on the double dynamic programming algorithm of Orengo and Taylor[2] was then combined with a new scoring function based on NER (Number of Equivalent Residues) by Daron M. Standley[3,4]. This page serves as a central portal where both web services and source code can be accessed.

ASH Web services

Dr. Toh's group at CBRC (Computational Biology Research Center) of AIST (Advanced industrial science and technology) provides tools for mapping functional information from alignments as well as the original versions of local and global ASH.

RASH Rapid ASH computes pair-wise alignments in under 1 second. RASH is generally sufficient if the structures are very similar.

GASH Genetic-algorithm ASH generates very accurate alignments in about twice the time as RASH. GASH is the best choice if the structures are only partially similar or if multiple solutions are required.

ASH Source Code

ASH 1.2 (fixed some long-standing bugs present in ver 1.0) is freely available. You must fill out a simple license agreement, then a link containing the source code will be sent to you by e-mail.